I've created a mask for a brain region of interest (2D 3x3 voxel square) and use that mask to extract values from different maps (i.e. FA map) of the whole brain. With fslmaths and fslstats, I can extract the range of values within my mask, mean value of my mask, etc., but I would like to extract the values for all 9 voxels in my ROI. Is that possible without having to draw 9 ROIs of 1 voxel each?
Commands I currently use:
fslmaths 'map-of-interest.nii.gz' -mas 'mask.nii.gz' 'output_file.nii.gz' #to create an output file of the map of interest with only the voxels included in the mask
fslstats output_file -R -M #returns range (min + max) and mean values for the ROI
I would like to obtain the FA for each of the 9 voxels in my ROI. The FSLstats/maths usage printouts do not specify functionalities to obtain values for all voxels within a mask, only functions that apply to the whole mask. Does anyone know a way to do/easily circumvent this issue?
Any tips would be greatly appreciated!
